CHAPTER 3
GENOME STRUCTURE AND ORGANISATION- GENERAL
The eukaryotic genome is safeguarded by the nuclear membrane from exposure to
cytoplasm. The constitution of nuclear genome of different organisms has different sequences,
variable amount of DNA and the number of chromosomes. However, certain features are
unique to eukaryotic genomes compared with prokaryotic genomes.
Major differences between prokaryotic and eukaryotic genomes
Characteristic Prokaryotes Eukaryotes
Genome size 600kb to 9.5 Mb 3 Mb to 140000 Mb
Average gene size/number 950bp/4300 2500bp/19000
Operon-like regulatory unit General No
Horizontal gene transfer Significant Negligible
Rate of non-coding sequences Low High
Intron Rare General
Redundant gene number Rare General
Ploidy level Haploidy Haploidy to Polyploidy
Chromosome number One More than one
Heterozygosity No Yes
The integrity of individual genes is being interrupted by multiple and identical copies of
particular sequences and large blocks of non-coding sequences. The characteristics of
eukaryotic genomes can be resolved by adopting various options to estimate the genome size
and expose the sequence complexity.
What is a genome?
The conventional definition of genome is number of chromosomes representing
haploidy. But the recent definition on a genome by Singer and Berg (1991) states the following:
The term genome is used to describe the totality of chromosomes (in molecular term DNA)
unique to a particular organism or any cell within the organism, as distinct from genotype,
which is the information contained within those chromosomes.
The first genomes to be studied in depth at the molecular level were those of the
bacterium Eschercia coli and its bacteriophage. The second group of genomes to be studied in
great detail at the molecular level were those of mitochondria and chloroplasts. Finally
attention has now turned to a detailed study of the nuclear genomes of selected eukaryotes:
yeast (Saccharomyces cerevisiae), a nematode (Caenorhabditis elegans), a mammal (Homo
sapiens) and plants (Arabidopsis thaliana) and rice (Oryza sativa).
Chromosome numbers and genome
Chromosomes are constructed of two broad classes of DNA - euchromatin and
heterochromatin. Euchromatin is really only a functional description usually assumed as
genetically active and less contracted than heterochromatin. Heterochromatin is region which
has repeated sequences which are transcriptionally inactive, but are important to the
functioning of chromosomes. These chromosomes constitute the genome of individual species
and the genomic constitution varies in different organisms. Cytological studies revealed that
not all chromosomes are similar and vary morphologically giving an option to categorize them
into different types.
With this variation in chromosome structure, the number of chromosomes in each
organism, otherwise called as ploidy level also varies. Double the dose of a genome [haploidy
(n) - single set of chromosomes] is expected as the normal ploidy level and the ploidy of an
organism having two sets of chromosomes is called as diploid (2n). The organisms having
chromosome numbers deviating from the diploid numbers, are heteroploid. Organisms are
classified as diploids and polyploids depending upon their chromosomes number. Those
having exactly the triple or higher multiples of the haploid number are called polyploids [triploid
(3n), tetraploid (4n), hexaploid (6n)]. Individuals with an increase or decrease of one or two
chromosomes over the multiples of haploid number are called with prefixes hyper and hypo
along the terms used to indicate their ploidy respectively (3n+1 - hypertriploid and 4n-1 -
hypotetraploid). Since this system of classification was confusing, more refined way of
classifying the individuals based on chromosomes number came into existence and is given
below.
Diploids Individuals having chromosomes double the number
of haploidy
Heteroploids Individuals with chromosomes deviating the diploid
number
Polyploids Individuals with chromosomes multiples of haploid
number, but more than diploid number (3n, 4n, 5n...)
Aneuploids Individuals with chromosomes deviating from the
exact multiples of the basic number (x+1, x+2, x-1,
x-2)
Whatever may be the number of chromosomes, the basic organization of the
chromosome is common for all organisms. DNA and basic proteins viz., histones are two major
components of chromosomes and the cell nucleus. During the process of evolution, a gradual
increase in the quantity of DNA, with minor adjustments (increase or decrease), has been
speculated at every step of evolution with increasing complexity. It is observed that DNA
content per nucleus in organisms at various levels of evolution increased with increasing
complexity
Nuclear DNA content and genomes
The total amount of DNA in the (haploid) genome is a characteristic of each living
species known as its C value. The fact that the DNA content of an organism is much greater
than that required to code for and regulate the production of all necessary proteins has been
termed the C value paradox. In eukaryotes, the C value is defined as the amount of DNA per
genome (1 C = haploid nucleus, 2C = dipliod nucleus and 4C = nucleus which is just about to
divide by mitosis). There is enormous variation in the range of C values, from as little as a
mere 106 bp for a mycoplasma to as much as 1011 bp for some plants and animals. The
following table summarizes the range of C values found in different plant species.
Species pg/2C Mbp/1C
Arabidopsis thaliana 0.30 145
Arachis hypogaea 5.83 2813
Brassica juncea 2.29 1105
Cicer arietinum 1.53 738
Glycine max 2.31 1115
Gossypium hirsutum 4.39 2118
Helainthus annuus 5.95 2871
Hordeum vulgare 10.10 4873
Lycopersicon esculentum 1.88 907
Oryza sativa 0.87 419
Phaselous vulgaris 1.32 637
Pisum sativum 8.18 3947
Saccharum officinarum 5.28 2547
Triticum aestivum 33.09 15966
Vigna mungo 1.19 574
Vigna radiata 1.20 579
Zea mays 4.75 2292
1 picogram (pg) = 965 Million base pairs (Mbp)
DNA sequences and genomes
DNA sequences can be divided into three groups depending on the number of times a
sequence appears in the genome.
1. Low or single copy DNA: These are sequences encoding most enzyme
functions. In general, these can constitute upto 50% of the total DNA.
2. Middle repeat DNA: These sequences code for most of the structural components
of a cell. Thirty to forty percent of the genome may comprise middle repeat DNA
3. Highly repetitious DNA: This is simple sequence DNA and is frequently non-
coding. In mammals, this can constitute 20-50% of the genome, but in many plants
this figure can exceed upto 80 percent. In general, DNA in the genome is arranged
with single copy sequences interspersed with either repetitive or middle repeat
DNA.
The complexity of any genome is assessed based on the proportion of above-
mentioned sequences.